Contacts of the strand formed by residues 1125 - 1137 (chain A) in PDB entry 3U44
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP1125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1123A ALA* 3.3 4.9 - - - +
1124A LYS* 1.3 81.2 - - + +
1126A LYS* 1.3 80.3 + - - +
1127A ASP* 4.0 26.7 - - + -
1130A ILE* 4.9 7.0 - - + -
1161A LEU* 4.1 18.8 - - + -
1162A TYR* 3.5 1.9 - - - +
1163A GLU* 3.0 58.1 + - + +
1168A LEU* 4.4 14.4 - - + -
31B PHE* 4.0 46.6 + + + +
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Residues in contact with LYS1126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073A LEU* 3.2 50.0 + - + +
1120A LEU* 3.3 19.8 + - + -
1121A ILE 2.8 25.7 + - - -
1123A ALA* 4.7 12.5 + - - -
1125A TRP* 1.3 92.1 + - - +
1127A ASP* 1.3 66.5 + - - +
1128A ARG* 6.0 1.1 - - + +
1160A CYS* 5.9 0.7 - - - -
1161A LEU 3.5 10.1 - - - +
1162A TYR* 4.4 7.9 - - + -
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Residues in contact with ASP1127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125A TRP* 4.0 18.2 - - + -
1126A LYS* 1.3 77.5 - - - +
1128A ARG* 1.3 84.9 + - - +
1130A ILE* 3.6 21.8 - - + +
1160A CYS* 4.2 0.7 - - - -
1161A LEU 3.0 31.8 + - - +
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Residues in contact with ARG1128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068A MET 3.4 14.2 + - - -
1069A GLN* 3.3 44.1 + - + +
1070A HIS 4.8 2.0 + - - -
1071A ILE 2.8 29.9 + - - -
1072A PRO* 5.1 0.6 - - - +
1073A LEU* 3.2 42.1 - - + +
1126A LYS* 6.0 1.0 - - - +
1127A ASP* 1.3 94.3 + - - +
1129A GLU* 1.3 76.6 + - + +
1130A ILE* 3.4 5.0 - - - +
1159A ASP 3.3 11.2 - - - +
1160A CYS* 4.0 13.0 - - - -
1173A TYR* 4.6 6.7 - - - -
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Residues in contact with GLU1129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065A HIS* 3.7 16.2 - - - -
1069A GLN* 2.7 44.4 + - + +
1128A ARG* 1.3 77.1 - - + +
1130A ILE* 1.3 59.5 + - - +
1131A PRO* 3.2 11.8 - - - +
1157A ILE* 3.8 32.0 - - + +
1158A ILE 3.8 3.6 - - - -
1159A ASP 3.0 12.7 + - - -
74B ARG* 3.8 13.6 + - - +
77B GLN* 4.0 28.7 + - - +
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Residues in contact with ILE1130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125A TRP* 4.9 4.7 - - + -
1127A ASP* 3.6 36.8 - - + +
1128A ARG 3.9 11.0 - - - +
1129A GLU* 1.3 75.1 - - - +
1131A PRO* 1.3 66.8 - - + +
1132A PHE* 3.8 2.9 + - + -
1157A ILE* 3.3 3.5 - - - +
1158A ILE* 2.8 48.2 + - + +
1161A LEU* 3.7 36.3 - - + +
31B PHE* 6.1 1.3 - - + -
61B ILE* 3.5 31.9 - - + -
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Residues in contact with PRO1131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129A GLU 3.2 8.5 - - - +
1130A ILE* 1.3 88.8 - - + +
1132A PHE* 1.3 61.6 + - - +
1156A GLY 3.5 8.1 - - - +
1157A ILE* 3.8 9.0 - - + -
61B ILE* 3.6 25.7 - - - +
63B ALA 5.6 0.2 - - - +
64B GLN* 3.1 34.4 - - + +
74B ARG* 3.1 27.6 - - - +
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Residues in contact with PHE1132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016A VAL* 5.9 1.6 - - + -
1130A ILE* 4.1 3.4 - - + +
1131A PRO* 1.3 75.4 - - - +
1133A SER* 1.3 68.2 + - - +
1134A LEU* 4.3 4.3 - - + -
1154A VAL* 3.8 21.8 - - + -
1155A GLN* 3.3 7.6 - - - +
1156A GLY* 3.0 65.0 + - - +
1158A ILE* 3.8 23.8 - - + -
1203A LEU* 4.6 7.0 - - + -
1204A TYR* 3.5 38.8 - + - -
1207A ALA* 3.5 28.3 - - + -
1211A ILE* 5.0 0.2 - - + -
60B MET 3.5 11.2 - - - +
61B ILE* 4.1 16.4 - - + -
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Residues in contact with SER1133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132A PHE* 1.3 75.8 - - - +
1134A LEU* 1.3 61.2 + - - +
1135A ALA 4.2 0.2 - - - -
1153A LEU* 4.2 8.1 - - - -
1154A VAL 3.6 4.0 - - - -
1155A GLN* 3.4 29.2 - - - -
1211A ILE* 3.3 3.5 - - - +
52B ALA* 4.2 3.1 - - - +
59B GLY* 3.1 19.6 - - - -
60B MET* 3.0 45.5 + - - +
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Residues in contact with LEU1134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132A PHE* 4.3 3.4 - - + -
1133A SER* 1.3 75.1 - - - +
1135A ALA* 1.3 63.0 + - - +
1136A LEU* 3.5 23.0 + - + -
1152A LEU 3.4 1.6 - - - +
1153A LEU* 4.4 2.9 - - - -
1154A VAL* 2.8 46.4 + - + +
1203A LEU* 4.0 11.9 - - + +
1206A LYS* 3.7 18.8 - - + -
1207A ALA* 3.7 42.4 - - + +
1210A GLN* 3.1 27.6 - - + +
1211A ILE* 4.1 9.2 - - + -
58B GLY 3.9 7.9 - - - +
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Residues in contact with ALA1135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1133A SER 4.2 0.6 - - - -
1134A LEU* 1.3 69.4 - - - +
1136A LEU* 1.3 68.7 + - - +
1137A PRO* 4.7 1.0 - - - +
1151A PRO* 4.2 18.6 - - + -
1152A LEU 3.4 7.6 - - - +
1153A LEU* 4.5 7.4 - - + +
1210A GLN* 4.2 13.0 + - - +
52B ALA* 3.9 18.5 - - + +
53B LYS* 5.8 0.2 - - - -
58B GLY* 2.9 32.7 + - - +
59B GLY* 4.5 0.4 - - - -
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Residues in contact with LEU1136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134A LEU* 4.0 20.0 - - + +
1135A ALA* 1.3 82.0 - - - +
1137A PRO* 1.3 76.6 - - + +
1140A GLU* 4.4 11.9 - - + +
1141A ILE* 3.6 22.7 - - + -
1151A PRO* 2.9 6.0 - - - +
1152A LEU* 2.7 51.6 + - + +
1154A VAL* 3.8 8.7 - - + -
1203A LEU* 3.6 28.3 - - + -
1206A LYS* 3.3 29.6 - - + +
1210A GLN* 4.4 2.5 - - - +
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Residues in contact with PRO1137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135A ALA 4.7 1.1 - - - +
1136A LEU* 1.3 93.0 - - + +
1138A ALA* 1.3 67.7 + - - +
1139A LYS* 4.4 7.0 - - + +
1140A GLU* 2.9 43.1 + - - +
1141A ILE 4.2 0.2 + - - -
1149A ASP* 4.0 27.1 - - + +
1150A GLU 4.1 0.4 - - - +
1151A PRO* 4.3 2.4 - - + -
1152A LEU* 3.8 3.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il